I am pretty sure USB is native for Thunderbolt 3, which means thunderbolt is now fully backward compatible with USB 2&3 interfaces. All you need is a cable adaptator wich won't cost you much (as opposed to thunderbolt 2 cables!).
Concerning audio interfaces and latencies, you can achive low latency on a usb or firewire interface if your interface drivers are great.
For example, I can have a rock solid 4ms roundtrip latency @48KHz on my babyface pro connected to usb and my PC.
I can even reach a 2.6ms roundtrip on my macbook pro 15 mid 2015, RME runing @192Khz.
on this computer (thunderbolt 2) i also tried to run a RME fireface 802, with a thunderbolt 2 to firewire cable. works pefectly.
I think thunderbolt 2 interfaces can be a LITTLE faster, but these connectors are already outdated, now that thunderbolt 3 merged with usb. so i think the better choice is to take a usb interface or wait for proper thunderbolt 3 interfaces if you want top notch latencies.
For now good old usb2 is not dead! i wouldn't bet the same for firewire or thunderbolt 2.